discreteKernelize           package:macat           R Documentation

_D_i_s_c_r_e_t_i_z_e _a_n_d _s_m_o_o_t_h _e_x_p_r_e_s_s_i_o_n _v_a_l_u_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     returns discretized kernelized expression values and saves them to
     a file if argument 'saveToFile' is TRUE.  For details on
     discretization see 'discretize'.

_U_s_a_g_e:

     discreteKernelize(data, chrom, margin = 10, step.width = 1e+05, kernel = rbf,
                       kernelparams = list(gamma = 1/10^13), saveToFile = TRUE)

_A_r_g_u_m_e_n_t_s:

    data: MACATData Object 

   chrom: chromosome to kernelize

  margin: symmetric qunatile in percent 

step.width: size of the interpolation steps 

  kernel: kernel function one of rbf, kNN, basePairDistance or your own 

kernelparams: list of named kernel parameters 

saveToFile: logicval indicating whether to write a flatfile or not 
          default is true

_D_e_t_a_i_l_s:

     Filename of the flatfile is: 
     'discrete_kernelized_seq_margin_<margin>_chrom_<chrom>.py' where
     <margin> is the discretization parameter and <chrom> the name of
     the chromosome.

_V_a_l_u_e:

     discretized and kernelized expression matrix

_A_u_t_h_o_r(_s):

     The MACAT Development team

_S_e_e _A_l_s_o:

     'pydata', 'kernelizeAll'

_E_x_a_m_p_l_e_s:

        #loaddatapkg("stjudem")
        data(stjd)
        discretizedKernelized = discreteKernelize(stjd, 13)

